Project Details

The innovative technology experience for students and teachers used in this project involves a “hands-on” cyber-learning approach, known as GENI-ACT, that will involve participants in a current and global research project while learning basic concepts of biology.

The GENI-ACT is a package of nine independent modules that will allow students and teachers to annotate a gene from a bacterium. Annotation is the process of assigning biologic function to to a gene. The 9 modules of GENI-ACT and their purpose are shown in the figure below:

The 9 Modules of GENI-ACT. The tools used in each module and the answers each module are meant to answer are shown. Click on the image to see a larger version.

Develop skills in making hypotheses and the design of experiments to test them

Sharpen skills in analysis, synthesis and in the presentation and interpretation of results

Experience the collaborative nature of science.

The project will target teacher populations as follows:

(i) the project will focus on educators of rural groups of students currently underrepresented in biomedical sciences, within counties primarily served by R-AHEC during its first year, including the Rochester NY Public School system.

(iii) the project will recruit educators of underrepresented students in urban and suburban school districts of Erie and Niagara counties served by EN-AHEC

(iv) the project will offer a select subset of enthusiastic teachers from each year the opportunity to continue for a second year to further hone their annotation skills and become “Master Annotation Teachers”. This additional level of training will allow this cohort of teachers to acquire a master level of proficiency that they can then utilize as ambassadors for the SEPA project, and aid in the recruiting, training and technical support of other educators.

The project is broken down into three main components:

Summer Teacher Training Workshop:

A summer training workshop for teachers who will subsequently guide their students to perform basic gene annotations later in the project will take place in July. Teachers will have a clinical focus to their training, by (i) receiving training in biomedical applications of bioinformatics during their summer training, and (ii) focusing on genes of clinical significance in human microbial pathogens (e.g. virulence genes, antibiotic resistance genes). The significance of annotation to novel gene discovery, to anchoring of metagenomic sequencing data and to the accuracy of gene calling from such a unique organism will be stressed. Experts in clinical bioinformatics or molecular diagnostic fields will participate in the teacher training workshop. The summer training workshop for teachers will have 5 continuous days of training in one week over the summer. Teachers will then come back to UB for the equivalent of 2 refresher training days in the fall to refresh their gene annotation skills prior to having them work with their students for the semester 2 gene annotation and then for another day in the spring to help them with the review of their students’ progress and to help them prepare for the final capstone poster presentations. Teachers still have a total of 8 days of training in the project and be paid for their time in training and in working with their students.

Semester 1 Activities:

The Semester 1 activities for the SEPA project will build student knowledge in the areas of molecular diagnostics and clinical genomics. We envision 5 activity modules to achieve this goal:

“Introduction to the Power of Molecular Diagnostics”, using a “Disease Detectives” approach and discussion of methodology

“Specific Application of Molecular Diagnostics to Disease”, using cystic fibrosis as an example.

“Ethics of DNA Testing”, in which students will be presented with scenarios dealing with ethical issues related to DNA testing and be encouraged to think about the impact it will have on their lives.

“Spotlight on Health Professionals and Genomics”, including videos of interviews with those individuals discussing how and why they entered the field. Students will be offered career guidance by AHEC facilitators at the end of this activity as well.

“Applications of Molecular Diagnostics” in relation to microbial infections. This module will include an introduction to the genome annotation activities in Semester 2.

Semester 2 Gene Annotation:

The project will involve gene annotation of prokaryotes. The organization of genes is simpler in prokaryotes and the complications of alternative splicing are avoided. Annotations of prokaryotic genes are therefore likely to be more easily grasped by high school level students.

The project will use genomes of multiple clinically significant microorganisms in Genbank as subjects for the annotation activities. These will be chosen to complement discussions in Semester 1 and will involve students doing research to generate background information about the organism, the types of infection it causes, the outcomes that result from infection and whether molecular diagnostic tests exist for their organism. Each school will be assigned a different organism on which to work. A mixture of genes will be selected from each organism for the students to annotate.

Examples of work on the genome annotation project performed by high school students and MS level students at the university at Buffalo can be seen in the Student Research page of this website.